ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.
|Date of publication||None|
|Maintainer||Peter Humburg <firstname.lastname@example.org>|
|License||GPL (>= 2)|
accessors: Access slots of S4 classes
alignFeature: Read counts relative to annotated features
BindScore: Class "BindScore"
callBindingSites: Predict protein binding sites from high-throughput sequencing...
ChIPseqR-package: Identifying Protein Binding Sites in High-Throughput...
compress-BindScore: Compress BindScore Objects
compress-methods: Methods for Function compress in Package 'ChIPseqR'
compress-ReadCounts: Compress ReadCount Objects
decompress: Extract Read Count and Binding Site Score Representations
decompress-methods: Methods for Function decompress in Package 'ChIPseqR'
exportBindSequence: Export sequence of predicted binding sites
getBindCor: Calculate cross-correlation between read counts
getBindLen: Estimate length of binding and support region
getCutoff: Determine significance threshold for binding site scores
internal: Internal and undocumented functions
pickPeak: Identify peaks above a given threshold
plot-BindScore: Diagnostic Plots for Binding Site Scores
plot-ReadCounts: Diagnostic Plots for Read Counts
plotReads: Plot compact representation of read counts on a chromosome
plotWindow: Plot read counts within a genomic region
pos2gff: Convert genome coordinates into GFF format
ReadCounts: Class "ReadCounts"
RLEBindScore-class: Run-length Encoded Binding Site Scores
RLEReadCounts-class: Run-length Encoded Read Counts
simpleNucCall: Predict nucleosome positions from high-throughput sequencing...
startScore: Score potential protein binding sites
strandPileup: Strand specific read counts
windowCounts: Summarize read counts in a sliding window